[Chimera-users] error running Antechamber

Eric Pettersen pett at cgl.ucsf.edu
Fri Jun 22 15:58:38 PDT 2007

Elaine's observation that Antechamber will not do a good job with  
metals is absolutely correct.  I would recommend editing your input  
file to put the colbalts into residues of their own.  This will allow  
Dock Prep to assign the proper charge to the metal (+2/+3) directly  
and run Antechamber on the remaining organic part of your ligand.  I  
intend to get Dock Prep to do this "metal separation" itself soon,  
but haven't gotten to it yet.

Also note that for large ligands (e.g. cobamamide) Antechamber can  
take many minutes to run on slower machines, so it's quite possible  
that what you thought was a "freeze" was in fact the charge  
calculation taking a while.  Try starting giving the calculation at  
least 10 minutes, and also checking if the "mopac" process is  
running, before deciding that the calculation is frozen.  If you do  
find a ligand that clearly freezes Chimera, send it to me and I'll  
look into the problem.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Jun 22, 2007, at 12:34 PM, Elaine Meng wrote:

> Hi SD,
> As I understand it, Antechamber is not meant to be used on metal
> complexes or on inorganic compounds. Trying to use it for such
> structures may give failures (as in your case) or unreasonable  
> results.
> Here is some text from the Antechamber website (
> http://amber.scripps.edu/antechamber/tips.html ):
> "Bondtype works for most of organic molecules that are made of C,  
> N, O,
> S, P, H, F, Cl, Br, I. It may not work well for high-charged molecules
> and molecules with too many unusual valence states."
> Bondtype is a routine in Antechamber; I believe the other routines  
> have
> similar restrictions.
> For structures not handled by Antechamber, it is necessary to use some
> other, outside program to calculate partial charges, or to find  
> them in
> the literature.  The charges can then be loaded into Chimera using
> Define Attribute (or the command "defattr") or by reading in a *.mol2
> file with charges in the charge column.  However, I guess you wouldn't
> need to use Dock Prep for that molecule if you already had a
> mol2-format file with the charges in it!
> I hope this makes things clearer,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> On Jun 22, 2007, at 10:55 AM, S Datta wrote:
>> Hi
>> I am trying to prep a ligand using chimera for
>> docking. When I try to add charges, one error which is
>> always present is "Atom whose IDATM type has no Sybyl
>> type: #-99.-99:1 at CO(type: Co).
>> At the end the reply log asks to check the total
>> charge and spin multiplicity.
>> When I manually change the total charge, after the
>> Atom error briefly appears, Chimera either freezes
>> (windows) or runs the program
>> /../antechamber/exe/mopac.sh (in linux) infinitely.
>> Could someone help me decipher what is going wrong ? I
>> tried to change the input format of the ligand file
>> from .pdb to .sy2 but that didnt help.
>> thanks a lot
>> SD
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